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Coding Skills

R
Python
Bash
AWK
SQL
Perl

Disclaimer

Made with the R package pagedown.

Based on the Nick Strayer’s CV package; modified source code for this CV is available here.

Last updated on 2021-03-11.

Main

Kasia Kedzierska

I am a 3rd year PhD student at the University of Oxford. I am a computational biologist, i.e., I use Data Science and Statistical Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression.

Selected Research Experience

DPhil Candidate

Wedge group and Church group

University of Oxford, UK

2022 - 2018

  • PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer

Visiting Graduate Student

Ratan group

University of Virginia, USA

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Research Assistant

Zebrafish Developmental Genomics

IIMCB, Warsaw, Poland

2016 - 2015

  • I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
  • I was responsible for both computational and experimental aspects of the project.

Education

DPhil. Candidate, Genomic Medicine and Statistics

Nuffield Department of Medicine, Brasenose College

University of Oxford, UK

2022 - 2018

M. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2018 - 2015

  • Thesis: Analysis of the mutational burden across gene sets in cancer.
  • Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.

Publications

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis

Clinical Epigenetics

2020

Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer

N. Horeweg, M. de Bruyn, R. A. Nout, E. Stelloo, K. Kedzierska, A. León-Castillo, A. Plat, K. D. Mertz, M. Osse, I. M. Jürgenliemk-Schulz, L. C.H.W. Lutgens, J. J. Jobsen, E. M. van der Steen-Banasik, V. T. Smit, C. L. Creutzberg, T. Bosse, H. W. Nijman, V. H. Koelzer and D. N. Church

Cancer Immunology Research

2020

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata

Genome Research

2019

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal

BMC Cancer

2018

SONiCS: PCR stutter noise correction in genome-scale microsatellites

K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler

Bioinformatics

2018

Selected Talks and Posters

Analysis of the mutational burden across gene sets in cancer

Polish Bioinformatics Society Symposium

Cracow, Poland

2019

  • Invited talk

Differential mutation analysis across gene sets in cancers

The Biology of Genomes 2018

Cold Spring Harbor, NY, USA

2018

  • Poster

Selected Awards and Honours

Senior Hulme Scholarship

N/A

N/A

2022 - 2021

  • Senior Hulme Scholarships is awarded by Brasenose College to DPhil students whose academic performance is deemed to be exceptional.

Best Master Thesis in Bioinformatics       

N/A

N/A

2019 - 2018

  • Analysis of the mutational burden across gene sets in cancer - Best Master Thesis defended in Bioinformatics in 2018 in Poland.

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College Londn

London, United Kingdom

2019

Teaching Experience

I like teaching and deeply believe in Open Science. With #NGSchool Society which I’m the president of, I’ve been organising Summer Schools in Bioinformatics. During #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. Nowadays, because of the pandemic, we switched to organising virtual events - NGSeminars series. We made all the content publicly available.

Online tutorials: Python for Data Science and Introduction to Python

NGSeminars

YouTube

2020

Introduction to Managing Code with Git

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2020 - 2019

Unsupervised learning, Introduction to Python

#NGSchool2019: Machine Learning for Biomedicine

Ostróda, Poland

2019

  • Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
  • Materials for the Introduction to Python are available on github

Introduction to R

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

Selected Grants

Visegrad Grant to organize #NGSchool2020 - postponed until 2021

Visegrad Fund

N/A

2021 - 2020

  • 32,190 EUR awarded towards organising #NGSchool2020 and #NGSymposium. Both events are postponed until 2021.

Non-profit Work

President

NGSchool Society

N/A

2021 - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019